Hsiang-Ju Chiu and Yi-Ju Tseng @ Chang Gung University
2019/08/23
4 Blocks in RStudio:
R : Core (iPhone)
install.packages("Package name")
library(Package name)
function_name(argument1, argument2,....)For example, we can get the average of numbers by mean() function:
mean(c(1,2,3,4,5,6)) ##average of 1~6
[1] 3.5
If you don't know the defined order, you can assign the arguments by name
seq(from=1,to=9,by=2)
[1] 1 3 5 7 9
install.packages("devtools")
devtools::install_github("DHLab-CGU/emr")
library(emr)
install.packages("tidyverse")
install.packages("tableone")
library(tidyverse)
library(tableone)
Explore the comorbidity or underlying diseases difference between patent ductus arteriosus (PDA) and the non-PDA patients
sampleFile_MIMIChead(sample_MIMICIII)
| SUBJECT_ID | HADM_ID | ROW_ID | SEQ_NUM | ICD9_CODE | ADMITTIME | ADMISSION_TYPE | DIAGNOSIS |
|---|---|---|---|---|---|---|---|
| 2 | 163353 | 1 | 1 | V3001 | 2138-07-17 | NEWBORN | NEWBORN |
| 2 | 163353 | 2 | 2 | V053 | 2138-07-17 | NEWBORN | NEWBORN |
| 2 | 163353 | 3 | 3 | V290 | 2138-07-17 | NEWBORN | NEWBORN |
| 5 | 178980 | 22 | 1 | V3000 | 2103-02-02 | NEWBORN | NEWBORN |
| 5 | 178980 | 23 | 2 | V053 | 2103-02-02 | NEWBORN | NEWBORN |
| 5 | 178980 | 24 | 3 | V290 | 2103-02-02 | NEWBORN | NEWBORN |
selectedPDA <-
selectCases(sample_MIMICIII,
SUBJECT_ID, ICD9_CODE,
ADMITTIME, "2015/10/01",
ICD, caseCondition = "^7470",
caseCount = 1,
CaseName = "PDA")
selectedPDA
| ID | selectedCase | count | firstCaseDate | endCaseDate | period | MostCommonICD | MostCommonICDCount |
|---|---|---|---|---|---|---|---|
| 32433 | PDA | 1 | 2201-01-11 | 2201-01-11 | 0 days | 7470 | 1 |
| 32603 | PDA | 1 | 2171-10-14 | 2171-10-14 | 0 days | 7470 | 1 |
| 32803 | PDA | 1 | 2118-02-06 | 2118-02-06 | 0 days | 7470 | 1 |
| 2 | non-PDA | NA | NA | NA | NA | NA | NA |
| 5 | non-PDA | NA | NA | NA | NA | NA | NA |
selectedPDA <-
selectCases(sample_MIMICIII,
SUBJECT_ID, ICD9_CODE,
ADMITTIME, "2015/10/01",
ICD, caseCondition = "^7470",
caseCount = 1,
CaseName = "PDA")
selectedPDA <-
selectCases(sample_MIMICIII,
SUBJECT_ID, ICD9_CODE,
ADMITTIME, "2015/10/01",
ICD, caseCondition = "^7470",
caseCount = 1,
CaseName = "PDA")
selectedPDA
| ID | selectedCase | count | firstCaseDate | endCaseDate | period | MostCommonICD | MostCommonICDCount |
|---|---|---|---|---|---|---|---|
| 32433 | PDA | 1 | 2201-01-11 | 2201-01-11 | 0 days | 7470 | 1 |
sample_MIMICIII[SUBJECT_ID=="32433"&
grepl("^747",ICD9_CODE)]
| SUBJECT_ID | ICD9_CODE | ADMITTIME |
|---|---|---|
| 32433 | 7470 | 2201-01-11 |
sample_MIMICIII[1:6,
c("SUBJECT_ID",
"ICD9_CODE", "ADMITTIME")]
| SUBJECT_ID | ICD9_CODE | ADMITTIME |
|---|---|---|
| 2 | V3001 | 2138-07-17 |
| 2 | V053 | 2138-07-17 |
| 2 | V290 | 2138-07-17 |
| 5 | V3000 | 2103-02-02 |
| 5 | V053 | 2103-02-02 |
| 5 | V290 | 2103-02-02 |
elix <-
groupedDataLongToWide(
sample_MIMICIII,SUBJECT_ID,
ICD9_CODE,ADMITTIME,
"9999-10-01", groupDataType = Elix,
isDescription = F,
selectedCaseFile = selectedPDA)
elix
| ID | ELIX_RENLFAIL | ELIX_TUMOR | ELIX_VALVE | ELIX_WGHTLOSS | selectedCase | |
|---|---|---|---|---|---|---|
| 17 | 70 | FALSE | FALSE | FALSE | FALSE | non-PDA |
| 18 | 72 | FALSE | FALSE | TRUE | FALSE | PDA |
| 19 | 74 | FALSE | FALSE | FALSE | FALSE | non-PDA |
| 20 | 82 | FALSE | FALSE | FALSE | FALSE | non-PDA |
| 21 | 87 | FALSE | FALSE | FALSE | FALSE | non-PDA |
plot_Elixhauser <- plot_groupedData(elix)
plot_Elixhauser$graph
plot_Elixhauser$sigCate
| DiagnosticCategory | Group | N | Percentage |
|---|---|---|---|
| ELIX_LYTES | non-PDA | 43 | 0.58% |
| ELIX_LYTES | PDA | 19 | 4.99% |
| ELIX_VALVE | non-PDA | 10 | 0.13% |
| ELIX_VALVE | PDA | 5 | 1.31% |
| ELIX_CHF | non-PDA | 4 | 0.05% |
| ELIX_CHF | PDA | 9 | 2.36% |
| ELIX_HTN | non-PDA | 6 | 0.08% |
| ELIX_HTN | PDA | 6 | 1.57% |
| ELIX_COAG | non-PDA | 7 | 0.09% |
| ELIX_COAG | PDA | 4 | 1.05% |
| ELIX_NEURO | non-PDA | 6 | 0.08% |
| ELIX_NEURO | PDA | 4 | 1.05% |
| ELIX_HYPOTHY | non-PDA | 5 | 0.07% |
| ELIX_HYPOTHY | PDA | 5 | 1.31% |
| ELIX_PULMCIRC | non-PDA | 1 | 0.01% |
| ELIX_PULMCIRC | PDA | 3 | 0.79% |
var_col <-
names(elix)[2:(length(elix)-1)]
table_Elix <-
CreateTableOne(vars = var_col,
strata = "selectedCase",
data = as.data.frame(elix),
factorVars = var_col)
table_Elix
| “non-PDA” | “PDA” | “p” | “test” | |
|---|---|---|---|---|
| “n” | 7452 | 381 | ||
| “ELIX_CHF = TRUE (%)” | 4 (0.1) | 9 (2.4) | <0.001 | |
| “ELIX_COAG = TRUE (%)” | 7 (0.1) | 4 (1.0) | <0.001 | |
| “ELIX_HTN = TRUE (%)” | 6 (0.1) | 6 (1.6) | <0.001 | |
| “ELIX_HYPOTHY = TRUE (%)” | 5 (0.1) | 5 (1.3) | <0.001 | |
| “ELIX_LYTES = TRUE (%)” | 43 (0.6) | 19 (5.0) | <0.001 | |
| “ELIX_NEURO = TRUE (%)” | 6 (0.1) | 4 (1.0) | <0.001 | |
| “ELIX_PULMCIRC = TRUE (%)” | 1 (0.0) | 3 (0.8) | <0.001 | |
| “ELIX_VALVE = TRUE (%)” | 10 (0.1) | 5 (1.3) | <0.001 |
sampleDxFile[6:10]
| ID | ICD | Date |
|---|---|---|
| A15 | Z992 | 2023-05-12 |
| A0 | 5855 | 2013-12-20 |
| A0 | V4511 | 2012-04-05 |
| A0 | V560 | 2010-03-28 |
| A0 | 5853 | 2010-10-29 |
| ICD code | ICD-9 | ICD-10 |
|---|---|---|
| Diagnosis | short and decimal format | short and decimal format |
| Procedure | short and decimal format | only decimal format |
| ICD code | ICD format | Code standardization |
|---|---|---|
| Clinical Classifications Software (CCS) | short format | IcdDxDecimalToShort |
| Phenome Wide Association Studies (PheWAS) | decimal format | IcdDxShortToDecimal |
| Comorbidity | short format | IcdDxDecimalToShort |
IcdDxShortToDecimalIcdDxDecimalToShortdecimal <-
IcdDxShortToDecimal(sampleDxFile, ICD,
Date, "2015/10/01")
short <-
IcdDxDecimalToShort(sampleDxFile, ICD,
Date, "2015/10/01")
cbind(decimal = decimal$ICD[6:10],
short = short$ICD[6:10])
| decimal.ICD | short.ICD |
|---|---|
| Z99.2 | Z992 |
| 585.5 | 5855 |
| V45.11 | V4511 |
| V56.0 | V560 |
| 585.3 | 5853 |
decimal$Error
| ICD | count | IcdVersionInFile | WrongType | Suggestion |
|---|---|---|---|---|
| A0.11 | 20 | ICD 10 | Wrong format | |
| V27.0 | 18 | ICD 10 | Wrong version | |
| E114 | 8 | ICD 10 | Wrong format | |
| A01.05 | 8 | ICD 9 | Wrong version | |
| 42761 | 7 | ICD 10 | Wrong version | |
| Z9.90 | 6 | ICD 10 | Wrong format | |
| F42 | 6 | ICD 10 | Wrong format | |
| V24.1 | 6 | ICD 10 | Wrong version | |
| A0105 | 5 | ICD 9 | Wrong version | |
| 001 | 5 | ICD 9 | Wrong format | 0019 |
| 75.52 | 4 | ICD 9 | Wrong format | |
| E03.0 | 4 | ICD 9 | Wrong version | |
| 650 | 4 | ICD 10 | Wrong version | |
| 123.45 | 3 | ICD 10 | Wrong format | |
| 755.2 | 3 | ICD 9 | Wrong format | 755.29 |
| 7552 | 2 | ICD 9 | Wrong format | 75529 |
We provide four strategies to group EHR diagnostic code.
After grouping, this package provides functions for querying matching cases, splitting data and generating condition era
Integrated EHR data:
IcdDxToCCS()IcdDxToCCSLvl()IcdDxToPheWAS()IcdDxToComorbid() IcdDxToCustom()IcdDxToCustomGrep()CCSlvl <-
IcdDxToCCSLvl(sampleDxFile,
ID, ICD, Date,
"2015-10-01", 2)
CCSlvl$groupedDT
| Short | ID | ICD | Date | CCS_LVL_2_LABEL |
|---|---|---|---|---|
| Z992 | A2 | Z992 | 2020-05-22 | Diseases of the urinary system |
| Z992 | A5 | Z992 | 2020-01-24 | Diseases of the urinary system |
| Z992 | A8 | Z992 | 2015-10-27 | Diseases of the urinary system |
| Z992 | A13 | Z992 | 2020-04-26 | Diseases of the urinary system |
| Z992 | A13 | Z992 | 2025-02-02 | Diseases of the urinary system |
| Z992 | A15 | Z992 | 2023-05-12 | Diseases of the urinary system |
CCSlvl$summarised_groupedDT
| ID | CCS_LVL_2_LABEL | firstCaseDate | endCaseDate | count | period |
|---|---|---|---|---|---|
| A0 | Diseases of the urinary system | 2009-07-25 | 2013-12-20 | 5 | 1609 days |
| A1 | Diseases of the urinary system | 2006-11-29 | 2014-09-24 | 5 | 2856 days |
| A10 | Diseases of the urinary system | 2007-11-04 | 2012-07-30 | 5 | 1730 days |
| A11 | Diseases of the urinary system | 2008-03-09 | 2011-09-03 | 5 | 1273 days |
| A12 | Diseases of the urinary system | 2006-05-14 | 2015-06-29 | 5 | 3333 days |
| A13 | Diseases of the urinary system | 2006-04-29 | 2025-02-02 | 5 | 6854 days |
CCS <-
IcdDxToCCS(sampleDxFile,
ID, ICD, Date,
"2015-10-01")
CCS$groupedDT
| Short | ID | ICD | Date | CCS_CATEGORY_DESCRIPTION |
|---|---|---|---|---|
| Z992 | A2 | Z992 | 2020-05-22 | Chronic kidney disease |
| Z992 | A5 | Z992 | 2020-01-24 | Chronic kidney disease |
| Z992 | A8 | Z992 | 2015-10-27 | Chronic kidney disease |
| Z992 | A13 | Z992 | 2020-04-26 | Chronic kidney disease |
| Z992 | A13 | Z992 | 2025-02-02 | Chronic kidney disease |
| Z992 | A15 | Z992 | 2023-05-12 | Chronic kidney disease |
CCS$summarised_groupedDT
| ID | CCS_CATEGORY_DESCRIPTION | firstCaseDate | endCaseDate | count | period |
|---|---|---|---|---|---|
| A0 | Chronic kidney disease | 2009-07-25 | 2013-12-20 | 5 | 1609 days |
| A1 | Chronic kidney disease | 2006-11-29 | 2014-09-24 | 5 | 2856 days |
| A10 | Chronic kidney disease | 2007-11-04 | 2012-07-30 | 5 | 1730 days |
| A11 | Chronic kidney disease | 2008-03-09 | 2011-09-03 | 5 | 1273 days |
| A12 | Chronic kidney disease | 2006-05-14 | 2015-06-29 | 5 | 3333 days |
| A13 | Chronic kidney disease | 2006-04-29 | 2025-02-02 | 5 | 6854 days |
case <-
selectCases(sampleDxFile, ID, ICD, Date,
"2015/10/01", ccslvl2,
caseCondition = "Diseases of the urinary system",
caseCount = 1,
CaseName = "Selected")
case[20:25]
| ID | selectedCase | count | firstCaseDate | endCaseDate | period | MostCommonICD | MostCommonICDCount |
|---|---|---|---|---|---|---|---|
| A5 | Selected | 5 | 2009-09-10 | 2020-01-24 | 3788 days | V420 | 1 |
| A6 | Selected | 5 | 2007-10-01 | 2015-07-12 | 2841 days | 5854 | 1 |
| A7 | Selected | 5 | 2007-02-01 | 2014-08-14 | 2751 days | 5854 | 1 |
| A8 | Selected | 5 | 2007-11-22 | 2015-10-27 | 2896 days | V561 | 1 |
| B2 | Selected | 6 | 2016-03-20 | 2024-09-20 | 3106 days | N189 | 1 |
| C0 | non-Selected | NA | NA | NA | NA | NA | NA |
recordDate <-
patientRecordDate(sampleDxFile, ID, ICD, Date)
recordDate
| ID | firstRecordDate | endRecordDate |
|---|---|---|
| A10 | 2007-11-04 | 2023-03-11 |
| A0 | 2009-07-25 | 2023-08-12 |
| C0 | 2015-12-05 | 2025-02-21 |
| B0 | 2015-12-26 | 2024-02-12 |
| D0 | 2017-01-29 | 2025-04-08 |
1-1. Wash-out and follow-up period <—–
WFPeriod<-merge(case,recordDate,by="ID")
WFPeriod[,list(ID,firstCaseDate,endCaseDate,
firstRecordDate,endRecordDate)]
| ID | firstCaseDate | endCaseDate | firstRecordDate | endRecordDate |
|---|---|---|---|---|
| A0 | 2009-07-25 | 2013-12-20 | 2009-07-25 | 2023-08-12 |
| A1 | 2006-11-29 | 2014-09-24 | 2006-11-29 | 2014-09-24 |
| A10 | 2007-11-04 | 2012-07-30 | 2007-11-04 | 2023-03-11 |
| A11 | 2008-03-09 | 2011-09-03 | 2008-03-09 | 2019-11-17 |
| A12 | 2006-05-14 | 2015-06-29 | 2006-01-12 | 2022-06-12 |
| A13 | 2006-04-29 | 2025-02-02 | 2006-04-29 | 2025-02-02 |
| A14 | 2006-11-28 | 2014-12-21 | 2006-11-28 | 2023-07-05 |
| A15 | 2007-05-25 | 2023-05-12 | 2007-05-25 | 2023-05-12 |
| A16 | 2007-04-15 | 2014-12-05 | 2007-04-15 | 2025-05-13 |
| A17 | 2007-02-19 | 2014-07-03 | 2007-02-19 | 2014-07-03 |
| A18 | 2007-04-05 | 2014-03-04 | 2007-04-05 | 2014-03-04 |
| A2 | 2011-09-20 | 2020-05-22 | 2011-09-20 | 2020-05-22 |
| A3 | 2008-07-08 | 2014-02-24 | 2008-07-08 | 2018-10-03 |
| A4 | 2006-10-20 | 2015-03-09 | 2006-10-20 | 2024-12-11 |
| A5 | 2009-09-10 | 2020-01-24 | 2009-09-10 | 2020-01-24 |
| A6 | 2007-10-01 | 2015-07-12 | 2007-10-01 | 2022-06-11 |
| A7 | 2007-02-01 | 2014-08-14 | 2007-02-01 | 2024-01-19 |
| A8 | 2007-11-22 | 2015-10-27 | 2007-11-22 | 2016-05-12 |
| A9 | 2007-03-05 | 2013-11-09 | 2006-06-30 | 2023-12-10 |
| B0 | 2015-12-26 | 2024-02-12 | 2015-12-26 | 2024-02-12 |
| B1 | 2016-08-08 | 2024-03-04 | 2014-06-30 | 2024-03-04 |
| B2 | 2016-03-20 | 2024-09-20 | 2016-03-20 | 2024-09-20 |
| B3 | 2019-05-07 | 2025-05-25 | 2012-12-24 | 2025-05-25 |
| B4 | 2015-12-02 | 2025-07-21 | 2007-11-19 | 2025-07-21 |
| C0 | NA | NA | 2015-12-05 | 2025-02-21 |
| C1 | NA | NA | 2010-12-03 | 2025-02-20 |
| C2 | NA | NA | 2009-12-16 | 2025-09-17 |
| C3 | NA | NA | 2014-03-26 | 2024-02-07 |
| C4 | NA | NA | 2015-11-23 | 2025-09-05 |
| D0 | NA | NA | 2017-01-29 | 2025-04-08 |
| D1 | NA | NA | 2006-02-12 | 2024-04-04 |
| D2 | NA | NA | 2006-09-01 | 2025-08-11 |
| D3 | NA | NA | 2013-03-14 | 2024-01-27 |
| D4 | NA | NA | 2007-09-23 | 2022-04-04 |
| D5 | NA | NA | 2013-07-16 | 2023-07-28 |
| D6 | NA | NA | 2005-10-09 | 2025-01-05 |
| D7 | NA | NA | 2007-05-22 | 2021-12-03 |
| D8 | NA | NA | 2007-01-30 | 2025-09-10 |
WFPeriod$Washout<-
WFPeriod$firstCaseDate-WFPeriod$firstRecordDate
WFPeriod$Followup<-
WFPeriod$endRecordDate-WFPeriod$firstCaseDate
WFPeriod[,list(ID,firstCaseDate,endCaseDate,
firstRecordDate,endRecordDate,
Washout,Followup)]
| ID | firstCaseDate | endCaseDate | firstRecordDate | endRecordDate | Washout | Followup |
|---|---|---|---|---|---|---|
| A0 | 2009-07-25 | 2013-12-20 | 2009-07-25 | 2023-08-12 | 0 days | 5131 days |
| A1 | 2006-11-29 | 2014-09-24 | 2006-11-29 | 2014-09-24 | 0 days | 2856 days |
| A10 | 2007-11-04 | 2012-07-30 | 2007-11-04 | 2023-03-11 | 0 days | 5606 days |
| A11 | 2008-03-09 | 2011-09-03 | 2008-03-09 | 2019-11-17 | 0 days | 4270 days |
| A12 | 2006-05-14 | 2015-06-29 | 2006-01-12 | 2022-06-12 | 122 days | 5873 days |
| A13 | 2006-04-29 | 2025-02-02 | 2006-04-29 | 2025-02-02 | 0 days | 6854 days |
| A14 | 2006-11-28 | 2014-12-21 | 2006-11-28 | 2023-07-05 | 0 days | 6063 days |
| A15 | 2007-05-25 | 2023-05-12 | 2007-05-25 | 2023-05-12 | 0 days | 5831 days |
| A16 | 2007-04-15 | 2014-12-05 | 2007-04-15 | 2025-05-13 | 0 days | 6603 days |
| A17 | 2007-02-19 | 2014-07-03 | 2007-02-19 | 2014-07-03 | 0 days | 2691 days |
| A18 | 2007-04-05 | 2014-03-04 | 2007-04-05 | 2014-03-04 | 0 days | 2525 days |
| A2 | 2011-09-20 | 2020-05-22 | 2011-09-20 | 2020-05-22 | 0 days | 3167 days |
| A3 | 2008-07-08 | 2014-02-24 | 2008-07-08 | 2018-10-03 | 0 days | 3739 days |
| A4 | 2006-10-20 | 2015-03-09 | 2006-10-20 | 2024-12-11 | 0 days | 6627 days |
| A5 | 2009-09-10 | 2020-01-24 | 2009-09-10 | 2020-01-24 | 0 days | 3788 days |
| A6 | 2007-10-01 | 2015-07-12 | 2007-10-01 | 2022-06-11 | 0 days | 5367 days |
| A7 | 2007-02-01 | 2014-08-14 | 2007-02-01 | 2024-01-19 | 0 days | 6196 days |
| A8 | 2007-11-22 | 2015-10-27 | 2007-11-22 | 2016-05-12 | 0 days | 3094 days |
| A9 | 2007-03-05 | 2013-11-09 | 2006-06-30 | 2023-12-10 | 248 days | 6124 days |
| B0 | 2015-12-26 | 2024-02-12 | 2015-12-26 | 2024-02-12 | 0 days | 2970 days |
| B1 | 2016-08-08 | 2024-03-04 | 2014-06-30 | 2024-03-04 | 770 days | 2765 days |
| B2 | 2016-03-20 | 2024-09-20 | 2016-03-20 | 2024-09-20 | 0 days | 3106 days |
| B3 | 2019-05-07 | 2025-05-25 | 2012-12-24 | 2025-05-25 | 2325 days | 2210 days |
| B4 | 2015-12-02 | 2025-07-21 | 2007-11-19 | 2025-07-21 | 2935 days | 3519 days |
| C0 | NA | NA | 2015-12-05 | 2025-02-21 | NA | NA |
| C1 | NA | NA | 2010-12-03 | 2025-02-20 | NA | NA |
| C2 | NA | NA | 2009-12-16 | 2025-09-17 | NA | NA |
| C3 | NA | NA | 2014-03-26 | 2024-02-07 | NA | NA |
| C4 | NA | NA | 2015-11-23 | 2025-09-05 | NA | NA |
| D0 | NA | NA | 2017-01-29 | 2025-04-08 | NA | NA |
| D1 | NA | NA | 2006-02-12 | 2024-04-04 | NA | NA |
| D2 | NA | NA | 2006-09-01 | 2025-08-11 | NA | NA |
| D3 | NA | NA | 2013-03-14 | 2024-01-27 | NA | NA |
| D4 | NA | NA | 2007-09-23 | 2022-04-04 | NA | NA |
| D5 | NA | NA | 2013-07-16 | 2023-07-28 | NA | NA |
| D6 | NA | NA | 2005-10-09 | 2025-01-05 | NA | NA |
| D7 | NA | NA | 2007-05-22 | 2021-12-03 | NA | NA |
| D8 | NA | NA | 2007-01-30 | 2025-09-10 | NA | NA |
1-1. Wash-out and follow-up period
2-1. Diagnosis before and after an important event <—–
These records can be used for a given patient as an index date for data split function.
indexDateTable <-
data.frame(ID = c("A0","B0","C0","D0"),
indexDate = c("2023-08-12",
"2024-02-12",
"2015-12-05",
"2017-01-29"),
stringsAsFactors = FALSE)
The important event, could be the first diagnosis date or treatment date
indexDateTable
| ID | indexDate |
|---|---|
| A0 | 2023-08-12 |
| B0 | 2024-02-12 |
| C0 | 2015-12-05 |
| D0 | 2017-01-29 |
certainPatient <-
sampleDxFile[grepl("A0|B0|C0|D0",ID),]
splitedData <-
splitDataByDate(certainPatient, ID, ICD, Date,
indexDateTable, Gap = 30)
splitedData[15:19,]
| ID | ICD | Date | indexDate | timeTag | window |
|---|---|---|---|---|---|
| B0 | N183 | 2023-08-28 | 2024-02-12 | B | 6 |
| B0 | N19 | 2023-11-18 | 2024-02-12 | B | 3 |
| B0 | N19 | 2024-02-12 | 2024-02-12 | A | 1 |
| C0 | C671 | 2015-12-05 | 2015-12-05 | A | 1 |
| C0 | C048 | 2016-07-05 | 2015-12-05 | A | 8 |
Diagnosis 180 days before the index date
splitedData[timeTag=="B"&window<=6,]
| ID | ICD | Date | indexDate | timeTag | window |
|---|---|---|---|---|---|
| B0 | N183 | 2023-08-28 | 2024-02-12 | B | 6 |
| B0 | N19 | 2023-11-18 | 2024-02-12 | B | 3 |
wideData <-
groupedDataLongToWide(sampleDxFile, ID,
ICD, Date,
"2015-10-01", elix,
isDescription = F)
wideData[,-(2:14))
| ID | ELIX_RENLFAIL | ELIX_TUMOR | ELIX_ULCER | ELIX_VALVE | ELIX_WGHTLOSS |
|---|---|---|---|---|---|
| A0 | TRUE | FALSE | FALSE | FALSE | FALSE |
| A1 | TRUE | FALSE | FALSE | FALSE | FALSE |
| A10 | TRUE | FALSE | FALSE | FALSE | FALSE |
| A11 | TRUE | FALSE | FALSE | FALSE | FALSE |
| A12 | TRUE | FALSE | FALSE | FALSE | FALSE |
| A13 | TRUE | FALSE | FALSE | FALSE | FALSE |
plotErrorICD <-
plot_errorICD(decimal$Error)
plotErrorICD$graph
plotErrorICD$ICD
| ICD | count | CumCountPerc | IcdVersionInFile | WrongType | Suggestion |
|---|---|---|---|---|---|
| A0.11 | 20 | 18.35% | ICD 10 | Wrong format | |
| V27.0 | 18 | 34.86% | ICD 10 | Wrong version | |
| E114 | 8 | 42.2% | ICD 10 | Wrong format | |
| A01.05 | 8 | 49.54% | ICD 9 | Wrong version | |
| 42761 | 7 | 55.96% | ICD 10 | Wrong version | |
| Z9.90 | 6 | 61.47% | ICD 10 | Wrong format | |
| F42 | 6 | 66.97% | ICD 10 | Wrong format | |
| V24.1 | 6 | 72.48% | ICD 10 | Wrong version | |
| A0105 | 5 | 77.06% | ICD 9 | Wrong version | |
| 001 | 5 | 81.65% | ICD 9 | Wrong format | 0019 |
| Others | 20 | 100% | ICD 9 | Wrong format |
plotGroupedData <-
plot_groupedData(wideData)
plotGroupedData$graph
Top 10 diagnostic categories grouped by Elixhauser comorbidity
plotGroupedData$sigCate
| DiagnosticCategory | N | Percentage |
|---|---|---|
| ELIX_RENLFAIL | 24 | 63.16% |
| ELIX_TUMOR | 6 | 15.79% |
| ELIX_ARTH | 5 | 13.16% |
| ELIX_LYMPH | 4 | 10.53% |
| ELIX_PSYCH | 4 | 10.53% |
| ELIX_DRUG | 3 | 7.89% |
| ELIX_NEURO | 3 | 7.89% |
| ELIX_PARA | 2 | 5.26% |
| ELIX_PERIVASC | 2 | 5.26% |
| ELIX_VALVE | 2 | 5.26% |
| ICD code | ICD-9 | ICD-10 |
|---|---|---|
| Diagnostic | short and decimal format | short and decimal format |
| Procedure | short and decimal format | only decimal format |
| ICD code | ICD format | Code standardization |
|---|---|---|
| CCS | short format | IcdDxDecimalToShort |
| procedure class | short format | IcdDxDecimalToShort |
samplePrFile[84:88]
| ID | ICD | Date |
|---|---|---|
| C | 0944 | 2008-10-26 |
| A | 19.6 | 2007-10-24 |
| C | 021R0ZA | 2020-04-09 |
| C | 008K3ZZ | 2020-02-27 |
| C | 0213093 | 2017-12-26 |
IcdPrShortToDecimalIcdPrDecimalToShortProcedureClass <-
IcdPrToProcedureClass(samplePrFile, ID, ICD,
Date, "2015-10-01")
ProcedureClass$groupedDT
| Short | ID | ICD | Date | PROCEDURE_CLASS_NAME |
|---|---|---|---|---|
| 5681 | B | 5681 | 2008-01-14 | Major Therapeutic |
| 9774 | A | 9774 | 2009-01-11 | Minor Therapeutic |
| 4499 | B | 44.99 | 2009-05-10 | Major Therapeutic |
| 0759 | C | 07.59 | 2009-01-21 | Major Therapeutic |
| 0205 | B | 0205 | 2008-07-06 | Major Therapeutic |
| 8812 | B | 8812 | 2007-06-27 | Minor Diagnostic |